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While trying to choose his next destination, the Doctor is suddenly aware of how dusty the TARDIS is, especially the console. The TARDIS, still in flight, is invaded by Koto. Koto is a bounty hunter, intent on absorbing every particle of light, heat and air from the TARDIS with his crystalline blue body. The Doctor demands to know why and is told Koto received a justice force auto-alert. The Doctor is wanted for his part in helping a war criminal escape from imprisonment. The Doctor explains the cell was empty, but Koto will hear no excuses. He begins absorption of the TARDIS to eliminate the Doctor before recapturing the prisoner.

As the sudden cold begins to bite, the Doctor changes into a yellow survival suit from the TARDIS wardrobe, where his old outfits are housed. Koto has absorbed all the heat from the TARDIS and the survival suit, so the Doctor rapidly cools down the bounty hunter with a fire extinguisher, a bucket of ice and a sudden snowstorm. Koto's sudden cooling down causes a short in the creature's thermal balance. This sends him back to where he came from. As the Doctor still puzzles over the “war criminal” reference, a face can be seen in the dust.

Supporting the series of collectible Doctor Who trading cards, the magazine carried a regular four-page, individually titled comic of the Tenth Doctor's adventures.

The artwork and colours were bold and bright, reflecting the tone of the magazine and, as did Doctor Who Adventures, reflected the appeal to readers younger than those catered to by Doctor Who Magazine.

The Battles in Time comic strip sought to reinforce the association of its Doctor with the one seen on screen with "props" from the TV series: blue/brown suit, sonic screwdriver, psychic paper and his intelligent glasses.

The TARDIS's winding DNA-like stairwell to the wardrobe area of the ship (first seen in The Christmas Invasion) shows the coats of the Doctor's first incarnations displayed on a hanging rail.